asniotest.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: asniotest.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:41:07  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: asniotest.cpp,v 1000.2 2004/06/01 19:41:07 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Authors:  Paul Thiessen
*
* File Description:
*      test suite for asn serialization library, asn data i/o
*
* ===========================================================================
*/

#include <ncbi_pch.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbitime.hpp>
#include <serial/serial.hpp>
#include <serial/objistrasn.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasn.hpp>
#include <serial/objostrasnb.hpp>
#include <util/random_gen.hpp>

#include <memory>

#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqloc/PDB_mol_id.hpp>
#include <objects/cdd/Cdd.hpp>
#include <objects/cdd/Global_id.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/mmdb1/Atom.hpp>
#include <objects/mmdb1/Atom_id.hpp>
#include <objects/mmdb2/Model_space_points.hpp>
#include <objects/mmdb3/Region_coordinates.hpp>
#include <objects/cn3d/Cn3d_color.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/id1/ID1server_maxcomplex.hpp>
#include <objects/id1/id1_client.hpp>

#include "asniotest.hpp"


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

// diagnostic streams
#define INFOMSG(stream) ERR_POST(Info << stream)
#define WARNINGMSG(stream) ERR_POST(Warning << stream)
#define ERRORMSG(stream) ERR_POST(Error << stream << '!')

// directory that contains test files (default overridden by env. var. ASNIOTEST_FILES)
string pathToFiles(".");

// keep track of files created, to remove them at the end
list < string > filesCreated;

// a utility function for reading different types of ASN data from a file
template < class ASNClass >
bool ReadASNFromFile(const char *filename, ASNClass *ASNobject, bool isBinary, string *err)
{
    err->erase();

    // initialize the binary input stream
    auto_ptr<CNcbiIstream> inStream;
    inStream.reset(new CNcbiIfstream(
        (pathToFiles + CDirEntry::GetPathSeparator() + filename).c_str(),
        IOS_BASE::in | IOS_BASE::binary));
    if (!(*inStream)) {
        *err = "Cannot open file for reading";
        return false;
    }

    auto_ptr<CObjectIStream> inObject;
    if (isBinary) {
        // Associate ASN.1 binary serialization methods with the input
        inObject.reset(new CObjectIStreamAsnBinary(*inStream));
    } else {
        // Associate ASN.1 text serialization methods with the input
        inObject.reset(new CObjectIStreamAsn(*inStream));
    }

    // Read the asn data
    bool okay = true;
    try {
        *inObject >> *ASNobject;
        INFOMSG("read file " << filename);
    } catch (exception& e) {
        *err = e.what();
        okay = false;
    }

    return okay;
}

// for writing out ASN data (to temporary files); all files written this way will be removed at program end
template < class ASNClass >
bool WriteASNToFile(const ASNClass& ASNobject, bool isBinary,
    string *err, EFixNonPrint fixNonPrint = eFNP_Default)
{
    err->erase();

    // construct a temp file name
    CNcbiOstrstream oss;
    oss << "test_" << (filesCreated.size() + 1) << (isBinary ? ".bin" : ".txt");
    string filename = CNcbiOstrstreamToString(oss);
    string fullPath = CDirEntry::MakePath(pathToFiles, filename);
    if (CFile(fullPath).Exists()) {
        WARNINGMSG("Overwriting temporary file " << fullPath);
        // *err = "Can't overwrite file ";
        // *err += fullPath;
        // return false;
    }

    // initialize a binary output stream
    auto_ptr<CNcbiOstream> outStream;
    outStream.reset(new CNcbiOfstream(
        fullPath.c_str(),
        isBinary ? (IOS_BASE::out | IOS_BASE::binary) : IOS_BASE::out));
    if (!(*outStream)) {
        *err = "Cannot open file for writing";
        return false;
    }
    filesCreated.push_back(fullPath);

    auto_ptr<CObjectOStream> outObject;
    if (isBinary) {
        // Associate ASN.1 binary serialization methods with the input
        outObject.reset(new CObjectOStreamAsnBinary(*outStream, fixNonPrint));
    } else {
        // Associate ASN.1 text serialization methods with the input
        outObject.reset(new CObjectOStreamAsn(*outStream, fixNonPrint));
    }

    // write the asn data
    bool okay = true;
    try {
        *outObject << ASNobject;
        outStream->flush();
        INFOMSG("wrote file " << filename);
    } catch (exception& e) {
        *err = e.what();
        okay = false;
    }

    return okay;
}

template < class ASNClass >
bool WriteASNToFilesTxtBin(const ASNClass& ASNobject, string *err)
{
    return (WriteASNToFile(ASNobject, false, err) && WriteASNToFile(ASNobject, true, err));
}

// test function macros
#define BEGIN_TEST_FUNCTION(func) \
    int func (void) { \
        int nErrors = 0; \
        string err; \
        INFOMSG("Running " #func " test");

#define END_TEST_FUNCTION \
        return nErrors; \
    }

#define ADD_ERR(msg) \
    do { \
        ERRORMSG(msg); \
        nErrors++; \
    } while (0)

#define ADD_ERR_RETURN(msg) \
    do { \
        ERRORMSG(msg); \
        nErrors++; \
        return nErrors; \
    } while (0)

#define SHOULD_THROW_EXCEPTION(object, accessor) \
    do { \
        try { \
            object.accessor(); \
            ADD_ERR(#accessor "() should have thrown an exception"); \
        } catch (exception& e) { \
            INFOMSG(#accessor "() correctly threw exception " << e.what()); \
        } \
    } while (0)


// tests reading and writing of asn data files
BEGIN_TEST_FUNCTION(BasicFileIO)

    // read in a trivial object
    CSeq_id seqId;
    if (!ReadASNFromFile("pdbSeqId.txt", &seqId, false, &err))
        ADD_ERR_RETURN("failed to load pdbSeqId.txt: " << err);

    // test text and binary output
    if (!WriteASNToFilesTxtBin(seqId, &err))
        ADD_ERR("failed to write CSeq_id: " << err);

    // now try a bigger object (in binary this time)
    CCdd cdd;
    if (!ReadASNFromFile("ADF.bin", &cdd, true, &err))
        ADD_ERR_RETURN("failed to load ADF.bin: " << err);
    if (!WriteASNToFilesTxtBin(cdd, &err))
        ADD_ERR("failed to write CCdd: " << err);

    // structure
    CNcbi_mime_asn1 mime;
    if (!ReadASNFromFile("1doi.bin", &mime, true, &err))
        ADD_ERR_RETURN("failed to load 1doi.bin: " << err);
    if (!WriteASNToFilesTxtBin(mime, &err))
        ADD_ERR("failed to write CNcbi_mime_asn1: " << err);

END_TEST_FUNCTION


// tests output of Assign()-copied objects
BEGIN_TEST_FUNCTION(AssignAndOutput)

    // try to output a copied simple object
    CSeq_id s1;
    if (!ReadASNFromFile("pdbSeqId.txt", &s1, false, &err))
        ADD_ERR_RETURN("failed to load pdbSeqId.txt: " << err);
    CSeq_id s2;
    s2.Assign(s1);
    if (!WriteASNToFilesTxtBin(s2, &err))
        ADD_ERR("failed to write Assign()'ed Seq-id: " << err);

    // try to output a copied complex object
    CCdd c1;
    if (!ReadASNFromFile("ADF.bin", &c1, true, &err))
        ADD_ERR_RETURN("failed to load ADF.bin: " << err);
    CCdd c2;
    c2.Assign(c1);
    if (!WriteASNToFilesTxtBin(c2, &err))
        ADD_ERR("failed to write Assign()'ed Cdd: " << err);

    // structure
    CNcbi_mime_asn1 m1;
    if (!ReadASNFromFile("1doi.bin", &m1, true, &err))
        ADD_ERR_RETURN("failed to load 1doi.bin: " << err);
    CNcbi_mime_asn1 m2;
    m2.Assign(m1);
    if (!WriteASNToFilesTxtBin(m2, &err))
        ADD_ERR("failed to write Assign()'ed Ncbi_mime_asn1: " << err);

END_TEST_FUNCTION


// tests operations and validations of a mandatory asn field (id and element from Atom)
BEGIN_TEST_FUNCTION(MandatoryField)

    // read in a good asn blob
    CAtom a1;
    if (!ReadASNFromFile("goodAtom.txt", &a1, false, &err))
        ADD_ERR_RETURN("failed to load goodAtom.txt: " << err);

    // try to read in a bad asn blob, missing a field - should fail
    INFOMSG("reading badAtom.txt - should fail");
    CAtom a2;
    if (ReadASNFromFile("badAtom.txt", &a2, false, &err))
        ADD_ERR_RETURN("badAtom.txt should not have loaded successfully");

    // Get/CanGet/Set/IsSet tests on loaded and created objects
    if (!a1.CanGetId() || !a1.IsSetId() || a1.GetId() != 37)
        ADD_ERR("id access failed");
    CAtom a3;
    if (a3.CanGetElement() || a3.IsSetElement())
        ADD_ERR("new Atom should not have element");
    SHOULD_THROW_EXCEPTION(a3, GetElement);
    a3.SetElement(CAtom::eElement_lr);
    if (!a3.CanGetElement() || !a3.IsSetElement() || a3.GetElement() != CAtom::eElement_lr)
        ADD_ERR("bad element state after SetElement()");

    // shouldn't be able to write without id
    INFOMSG("trying to write incomplete Atom - should fail");
    if (WriteASNToFilesTxtBin(a3, &err))
        ADD_ERR("should not be able to write Atom with no id");
    a3.SetId().Set(92);
    if (!WriteASNToFilesTxtBin(a3, &err))
        ADD_ERR("failed to write complete Atom: " << err);

END_TEST_FUNCTION


// test list (SEQUENCE) field
BEGIN_TEST_FUNCTION(ListField)

    // read in a valid object, with a mandatory but empty list
    CModel_space_points m1;
    if (!ReadASNFromFile("goodMSP.txt", &m1, false, &err))
        ADD_ERR_RETURN("failed to read goodMSP.txt: " << err);
    if (!m1.IsSetX() || !m1.CanGetX() || m1.GetX().size() != 3 || m1.GetX().front() != 167831)
        ADD_ERR("x access failed");
    if (!m1.IsSetZ() || !m1.CanGetZ() || m1.GetZ().size() != 0)
        ADD_ERR("z access failed");

    // test created object
    CModel_space_points m2;
    if (m2.IsSetX() || !m2.CanGetX() || m2.GetX().size() != 0)
        ADD_ERR_RETURN("bad x state in new object");